Multiplex PCR-Based Nanopore Sequencing and Epidemiological Surveillance of Hantaan orthohantavirus in Apodemus agrarius, Republic of Korea
- Authors
- Park, Kyungmin; Lee, Seung-Ho; Kim, Jongwoo; Lee, Jingyeong; Lee, Geum-Young; Cho, Seungchan; Lee, Seung Ho; Park, Kkothanahreum; No, Jin Sun; Budhathoki, Shailesh; Kim, Yu-Jin; Kim, Young-Su; Kim, Heung-Chul; Klein, Terry A.; Kim, Won-Keun; Song, Jin-Won
- Issue Date
- 5월-2021
- Publisher
- MDPI
- Keywords
- Hantaan virus (HTNV); hemorrhagic fever with renal syndrome (HFRS); next-generation sequencing (NGS); whole-genome sequencing; amplicon-based NGS; MinION sequencing; phylogenetic analysis; genetic diversity; viral genome surveillance
- Citation
- VIRUSES-BASEL, v.13, no.5
- Indexed
- SCIE
SCOPUS
- Journal Title
- VIRUSES-BASEL
- Volume
- 13
- Number
- 5
- URI
- https://scholar.korea.ac.kr/handle/2021.sw.korea/128182
- DOI
- 10.3390/v13050847
- ISSN
- 1999-4915
- Abstract
- Whole-genome sequencing of infectious agents enables the identification and characterization of emerging viruses. The MinION device is a portable sequencer that allows real-time sequencing in fields or hospitals. Hantaan orthohantavirus (Hantaan virus, HTNV), harbored by Apodemus agrarius, causes hemorrhagic fever with renal syndrome (HFRS) and poses a critical public health threat worldwide. In this study, we aimed to evaluate the feasibility of using nanopore sequencing for whole-genome sequencing of HTNV from samples having different viral copy numbers. Amplicon-based next-generation sequencing was performed in A. agrarius lung tissues collected from the Republic of Korea. Genomic sequences of HTNV were analyzed based on the viral RNA copy numbers. Amplicon-based nanopore sequencing provided nearly full-length genomic sequences of HTNV and showed sufficient read depth for phylogenetic analysis after 8 h of sequencing. The average identity of the HTNV genome sequences for the nanopore sequencer compared to those of generated from Illumina MiSeq revealed 99.8% (L and M segments) and 99.7% (S segment) identities, respectively. This study highlights the potential of the portable nanopore sequencer for rapid generation of accurate genomic sequences of HTNV for quicker decision making in point-of-care testing of HFRS patients during a hantavirus outbreak.
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Collections - Graduate School > Department of Biomedical Sciences > 1. Journal Articles
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